Setup conda for Python and R virtual environments¶
Automated installation using our installer program¶
Step 1¶
Log into stargate with a terminal.
Step 2¶
Run the installer:
install_conda
Step 3¶
Log out and back in for the changes to take effect.
Manual installation on the computing cluster¶
Step 1¶
Log into stargate with a terminal.
Step 2¶
Download Miniconda:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
Step 3¶
Make the installer executable:
chmod 755 Miniconda3-latest-Linux-x86_64.sh
Step 4¶
Run the installer:
./Miniconda3-latest-Linux-x86_64.sh -b -f -u
Note
Step 5 is optional. It is useful if you plan on running non-interactive
jobs in the cluster that rely on a conda environment. The goal is to move
the conda
hook code from the shell login profile .bashrc
to the more
general Bash profile .bash_profile
. Non-interactive jobs in the cluster
only load the profile .bash_profile
, while interactive jobs load both
profiles.
Edit the file .bashrc
using nano
, emacs
, or vim
(e.g. nano .bashrc
).
Highlight and copy the following code (note: your username will be in place of
user
below) and then delete it.
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/user/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/home/user/miniconda3/etc/profile.d/conda.sh" ]; then
. "/home/user/miniconda3/etc/profile.d/conda.sh"
else
export PATH="/home/user/miniconda3/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda initialize <<<
Step 6¶
Edit the file .bash_profile
using nano
, emacs
, or vim
(e.g.
nano .bash_profile
). Paste the copied code block above at the bottom of this
file (if doing Step 5). Add the following line to the file:
export PYTHONPATH=""
Step 7¶
Log out and back in for the changes to take effect.
Installation on your local computer¶
Step 1¶
Navigate to the Miniconda download page with your web browser.
Step 2¶
Under the section Latest Miniconda Installer Links, click on the appropriate link for your computer. Typically you want Miniconda3 Windows 64-bit, Miniconda3 MacOSX 64-bit pkg, or Miniconda3 Linux 64-bit.
Step 3¶
Run the installer and allow Miniconda to be activated by default (if prompted).
Step 4¶
Log out and back in for the changes to take effect.